diff --git a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/AndroidToolchain.java b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/AndroidToolchain.java
index a6cfe93d..fd23f807 100644
--- a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/AndroidToolchain.java
+++ b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/AndroidToolchain.java
@@ -81,13 +81,13 @@ public void compile () {
 
         StringBuilder headerDirs = new StringBuilder();
         for (String headerDir : target.headerDirs) {
-            headerDirs.append(convertPathToAbsolute(headerDir).getAbsolutePath());
+            headerDirs.append(convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
             headerDirs.append(" ");
         }
-        headerDirs.append("jni-headers");
-        headerDirs.append(" jni-headers/" + target.os.getJniPlatform());
-        headerDirs.append(" jni-headers/" + "linux");
-        headerDirs.append(" .");
+        headerDirs.append(convertToAbsoluteRelativeTo(config.jniDir, "jni-headers"));
+        headerDirs.append(" " + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        headerDirs.append(" " + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + "linux"));
+        headerDirs.append(" " + convertToAbsoluteRelativeTo(config.jniDir, "."));
 
         template = template.replace("%sharedLibName%", config.sharedLibName);
         template = template.replace("%headerDirs%", headerDirs);
@@ -102,7 +102,7 @@ public void compile () {
 
         ArrayList<String> args = new ArrayList<>();
         args.add("NDK_PROJECT_PATH=" + buildDirectory.getAbsolutePath());
-        args.add("NDK_APPLICATION_MK =" + new File(buildDirectory, "Application.mk").getAbsolutePath());
+        args.add("NDK_APPLICATION_MK=" + new File(buildDirectory, "Application.mk").getAbsolutePath());
         args.add("APP_BUILD_SCRIPT=" + new File(buildDirectory, "Android.mk").getAbsolutePath());
         args.add("NDK_OUT=" + buildDirectory.getAbsolutePath());
         args.add("NDK_LIBS_OUT=" + libsDirectory.getAbsolutePath());
diff --git a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/BaseToolchain.java b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/BaseToolchain.java
index 8663b6d0..64cb87da 100644
--- a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/BaseToolchain.java
+++ b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/BaseToolchain.java
@@ -3,6 +3,7 @@
 import com.badlogic.gdx.jnigen.AntPathMatcher;
 import com.badlogic.gdx.jnigen.BuildConfig;
 import com.badlogic.gdx.jnigen.BuildTarget;
+import com.badlogic.gdx.jnigen.FileDescriptor;
 import com.badlogic.gdx.jnigen.build.RuntimeEnv;
 import com.badlogic.gdx.jnigen.build.ToolchainExecutor;
 import org.slf4j.Logger;
@@ -16,7 +17,6 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
-import java.util.stream.Collectors;
 
 public abstract class BaseToolchain {
 
@@ -208,13 +208,13 @@ public FileVisitResult postVisitDirectory (Path dir, IOException exc) {
 
 
 
-    protected File convertPathToAbsolute (String path) {
+    protected File convertToAbsoluteRelativeTo (FileDescriptor rootRelative, String path) {
         //Path might be a relative path or an absolute, if its absolute just wrap, otherwise convert it to absolute
         //based around our project directory
 
         File file = new File(path);
         if (!file.isAbsolute()) {
-            file = new File(config.projectDir.file(), path);
+            file = new File(rootRelative.file(), path);
         } else {
             file = file.getAbsoluteFile();
         }
diff --git a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/GNUToolchain.java b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/GNUToolchain.java
index 569a69ab..2b807111 100644
--- a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/GNUToolchain.java
+++ b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/GNUToolchain.java
@@ -8,7 +8,6 @@
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -60,12 +59,12 @@ private void compileC () {
 
         List<String> args = new ArrayList<>();
         args.addAll(stringFlagsToArgs(target.cFlags));
-        args.add("-Ijni-headers");
-        args.add("-Ijni-headers/" + target.os.getJniPlatform());
-        args.add("-I.");
 
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/"));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("-I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("-I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
         ArrayList<String> perFileArgs = new ArrayList<String>();
@@ -92,12 +91,12 @@ private void compileCPP () {
 
         List<String> args = new ArrayList<>();
         args.addAll(stringFlagsToArgs(target.cppFlags));
-        args.add("-Ijni-headers/");
-        args.add("-Ijni-headers/" + target.os.getJniPlatform());
-        args.add("-I.");
 
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/"));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("-I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("-I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
         ArrayList<String> perFileArgs = new ArrayList<String>();
diff --git a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/IOSToolchain.java b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/IOSToolchain.java
index 8c260d29..a228403c 100644
--- a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/IOSToolchain.java
+++ b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/IOSToolchain.java
@@ -3,14 +3,12 @@
 import com.badlogic.gdx.jnigen.build.ToolFinder;
 import com.badlogic.gdx.jnigen.build.ToolchainExecutor;
 import com.badlogic.gdx.utils.Architecture;
-import com.badlogic.gdx.utils.Os;
 import com.badlogic.gdx.utils.TargetType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -85,15 +83,15 @@ private void compileC () {
 
         args.addAll(stringFlagsToArgs(target.cFlags));
 
-
-        args.add("-Ijni-headers");
-        args.add("-Ijni-headers/" + target.os.getJniPlatform());
-        args.add("-I.");
-        args.add("-g");
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers"));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("-I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("-I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
+        args.add("-g");
+
         ArrayList<String> perFileArgs = new ArrayList<String>();
         perFileArgs.addAll(args);
 
@@ -134,14 +132,15 @@ private void compileCPP () {
         args.addAll(stringFlagsToArgs(target.cppFlags));
 
 
-        args.add("-Ijni-headers");
-        args.add("-Ijni-headers/" + target.os.getJniPlatform());
-        args.add("-I.");
-        args.add("-g");
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers"));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("-I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("-I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("-I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
+        args.add("-g");
+
         ArrayList<String> perFileArgs = new ArrayList<String>();
         perFileArgs.addAll(args);
 
diff --git a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/MSVCToolchain.java b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/MSVCToolchain.java
index 66649e80..39b12137 100644
--- a/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/MSVCToolchain.java
+++ b/gdx-jnigen/src/main/java/com/badlogic/gdx/jnigen/build/toolchains/MSVCToolchain.java
@@ -9,7 +9,6 @@
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -204,11 +203,11 @@ private void compileC () {
         for (String msvcIncludeDirectory : msvcIncludeDirectories) {
             args.add("/I" + msvcIncludeDirectory);
         }
-        args.add("/Ijni-headers");
-        args.add("/Ijni-headers/" + target.os.getJniPlatform());
-        args.add("/I.");
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers"));
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("/I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("/I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
         ArrayList<String> perFileArgs = new ArrayList<String>();
@@ -239,11 +238,11 @@ private void compileCPP () {
         for (String msvcIncludeDirectory : msvcIncludeDirectories) {
             args.add("/I" + msvcIncludeDirectory);
         }
-        args.add("/Ijni-headers");
-        args.add("/Ijni-headers/" + target.os.getJniPlatform());
-        args.add("/I.");
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers"));
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "jni-headers/" + target.os.getJniPlatform()));
+        args.add("/I" + convertToAbsoluteRelativeTo(config.jniDir, "."));
         for (String headerDir : target.headerDirs) {
-            args.add("/I" + convertPathToAbsolute(headerDir).getAbsolutePath());
+            args.add("/I" + convertToAbsoluteRelativeTo(config.projectDir, headerDir).getAbsolutePath());
         }
 
         ArrayList<String> perFileArgs = new ArrayList<String>();